chore(deps): update dependency lambdaisland/kaocha to v1.91.1392 #5867
Workflow file for this run
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| name: Build | |
| on: | |
| schedule: | |
| - cron: '0 10 * * *' # every day at 10am | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| tags: | |
| - 'v*.*.*' | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| jobs: | |
| fmt: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| cljfmt: 0.12.0 | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Check Formatting | |
| run: make fmt | |
| lint: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| clj-kondo: '2024.03.13' | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Lint | |
| run: make lint | |
| test: | |
| strategy: | |
| matrix: | |
| module: | |
| - admin-api | |
| - anomaly | |
| - async | |
| - byte-buffer | |
| - byte-string | |
| - cassandra | |
| - coll | |
| - cql | |
| - db | |
| - db-resource-store | |
| - db-resource-store-cassandra | |
| - db-tx-log | |
| - db-tx-log-kafka | |
| - executor | |
| - extern-terminology-service | |
| - fhir-client | |
| - fhir-path | |
| - fhir-structure | |
| - http-client | |
| - interaction | |
| - jepsen | |
| - job-re-index | |
| - job-scheduler | |
| - kv | |
| - luid | |
| - metrics | |
| - module-base | |
| - openid-auth | |
| - operation-graphql | |
| - operation-measure-evaluate-measure | |
| - operation-patient-everything | |
| - operation-totals | |
| - page-store | |
| - page-store-cassandra | |
| - rest-api | |
| - rest-util | |
| - rocksdb | |
| - scheduler | |
| - server | |
| - thread-pool-executor-collector | |
| java-version: | |
| - '11' | |
| - '17' | |
| - '21' | |
| exclude: | |
| - module: jepsen | |
| java-version: '11' | |
| - module: jepsen | |
| java-version: '17' | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Java | |
| uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: ${{ matrix.java-version }} | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| cli: '1.11.2.1446' | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ matrix.module }}-${{ hashFiles(format('modules/{0}/deps.edn', matrix.module)) }} | |
| - name: Test | |
| run: make -C modules/${{ matrix.module }} test | |
| test-root: | |
| strategy: | |
| matrix: | |
| java-version: | |
| - '11' | |
| - '17' | |
| - '21' | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Java | |
| uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: ${{ matrix.java-version }} | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| cli: '1.11.2.1446' | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-temurin-${{ matrix.java-version }}-maven-${{ hashFiles('deps.edn') }} | |
| - name: Test | |
| run: make test-root | |
| build: | |
| needs: [ fmt, lint, test, test-root ] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Java | |
| uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '17' | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| cli: '1.11.2.1446' | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-temurin-17-maven-build-${{ hashFiles('**/deps.edn') }} | |
| - name: Build Uberjar | |
| run: make uberjar | |
| - name: Upload Blaze Uberjar | |
| uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
| with: | |
| name: blaze-uberjar | |
| path: target/blaze-*-standalone.jar | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@d70bba72b1f3fd22344832f00baa16ece964efeb # v3 | |
| - name: Build and Export to Docker | |
| uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5 | |
| with: | |
| context: . | |
| tags: blaze:latest | |
| outputs: type=docker,dest=/tmp/blaze.tar | |
| - name: Upload Blaze Image | |
| uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp/blaze.tar | |
| build-frontend: | |
| needs: [ fmt, lint ] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Setup Node | |
| uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: 21 | |
| - name: Build Frontend | |
| run: make build-frontend | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@d70bba72b1f3fd22344832f00baa16ece964efeb # v3 | |
| - name: Build and Export to Docker | |
| uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5 | |
| with: | |
| context: modules/frontend | |
| tags: blaze-frontend:latest | |
| outputs: type=docker,dest=/tmp/blaze-frontend.tar | |
| - name: Upload Blaze Image | |
| uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
| with: | |
| name: blaze-frontend-image | |
| path: /tmp/blaze-frontend.tar | |
| image-scan: | |
| needs: [ build, build-frontend ] | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| security-events: write | |
| strategy: | |
| matrix: | |
| image: | |
| - blaze | |
| - blaze-frontend | |
| steps: | |
| - name: Download Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: ${{ matrix.image }}-image | |
| path: /tmp | |
| - name: Load Image | |
| run: docker load --input /tmp/${{ matrix.image }}.tar | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Run Trivy Vulnerability Scanner | |
| uses: aquasecurity/trivy-action@master | |
| with: | |
| image-ref: ${{ matrix.image }}:latest | |
| format: sarif | |
| output: trivy-results.sarif | |
| severity: 'CRITICAL,HIGH' | |
| timeout: '15m0s' | |
| - name: Upload Trivy Scan Results to GitHub Security Tab | |
| if: ${{ (github.repository_owner == 'samply') || (vars.IMAGE_SCAN_UPLOAD == 'true') }} | |
| uses: github/codeql-action/upload-sarif@9fdb3e49720b44c48891d036bb502feb25684276 # v3 | |
| with: | |
| sarif_file: trivy-results.sarif | |
| integration-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| variant: | |
| - standalone | |
| - distributed | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 -p 8081:8081 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| if: ${{ matrix.variant == 'standalone' }} | |
| - name: Run Kafka, Cassandra and Blaze | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml up -d | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| if: ${{ matrix.variant == 'standalone' }} | |
| - name: Wait for Blaze 1 | |
| run: .github/scripts/wait-for-url.sh http://localhost:8081/metrics | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Wait for Blaze 2 | |
| run: .github/scripts/wait-for-url.sh http://localhost:8082/metrics | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| if: ${{ matrix.variant == 'standalone' }} | |
| - name: Docker Logs Kafka | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs kafka | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Logs Cassandra 1 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs cassandra-1 | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Logs Cassandra 2 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs cassandra-2 | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Logs Blaze 1 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs blaze-1 | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Logs Blaze 2 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs blaze-2 | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Stats | |
| run: docker stats --no-stream | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Check Capability Statement Filtered by _elements | |
| run: .github/scripts/check-capability-statement-filtered.sh | |
| - name: Check Capability Statement Caching | |
| run: .github/scripts/check-capability-statement-caching.sh | |
| - name: Check Referential Integrity Enforced | |
| run: .github/scripts/check-referential-integrity-enforced.sh | |
| - name: Load Data | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea | |
| - name: Check Total-Number of Resources are 92114 | |
| run: .github/scripts/check-total-number-of-resources.sh 92114 | |
| - name: Check Resource Totals | |
| run: .github/scripts/check-resource-totals.sh | |
| - name: Count Resources | |
| run: blazectl count-resources --server http://localhost:8080/fhir | |
| - name: Download All Resources | |
| run: .github/scripts/download-all-resources.sh | |
| - name: Download Patient Resources | |
| run: .github/scripts/download-resources.sh Patient | |
| - name: Download Male Patient Resources | |
| run: .github/scripts/download-resources-query.sh Patient "gender=male" 56 | |
| - name: Download Female Patient Resources | |
| run: .github/scripts/download-resources-query.sh Patient "gender=female" 64 | |
| - name: Download Patient Resources - Including Observation, Condition, Encounter and Procedure | |
| run: .github/scripts/revinclude.sh | |
| - name: Download Observation Resources | |
| run: .github/scripts/download-resources.sh Observation | |
| - name: Download Observation Resources with special LOINC Codes | |
| run: .github/scripts/download-resources-query.sh Observation "code=http://loinc.org|10230-1,http://loinc.org|10480-2,http://loinc.org|10834-0,http://loinc.org|14804-9,http://loinc.org|14959-1,http://loinc.org|1742-6,http://loinc.org|1751-7,http://loinc.org|17861-6,http://loinc.org|18262-6,http://loinc.org|19123-9" 2399 | |
| - name: Download Observation Resources with all LOINC Codes | |
| run: .github/scripts/download-resources-query.sh Observation "_count=500&code=http://loinc.org|10230-1,http://loinc.org|10480-2,http://loinc.org|10834-0,http://loinc.org|14804-9,http://loinc.org|14959-1,http://loinc.org|1742-6,http://loinc.org|1751-7,http://loinc.org|17861-6,http://loinc.org|18262-6,http://loinc.org|19123-9,http://loinc.org|1920-8,http://loinc.org|1960-4,http://loinc.org|1975-2,http://loinc.org|1988-5,http://loinc.org|19926-5,http://loinc.org|19994-3,http://loinc.org|2019-8,http://loinc.org|2028-9,http://loinc.org|20454-5,http://loinc.org|20505-4,http://loinc.org|20565-8,http://loinc.org|20570-8,http://loinc.org|2069-3,http://loinc.org|2075-0,http://loinc.org|2085-9,http://loinc.org|2093-3,http://loinc.org|21000-5,http://loinc.org|2157-6,http://loinc.org|2160-0,http://loinc.org|21905-5,http://loinc.org|21906-3,http://loinc.org|21907-1,http://loinc.org|21908-9,http://loinc.org|2276-4,http://loinc.org|2339-0,http://loinc.org|2345-7,http://loinc.org|2498-4,http://loinc.org|2500-7,http://loinc.org|2502-3,http://loinc.org|2514-8,http://loinc.org|2532-0,http://loinc.org|25428-4,http://loinc.org|2571-8,http://loinc.org|26881-3,http://loinc.org|2703-7,http://loinc.org|2708-6,http://loinc.org|2713-6,http://loinc.org|2744-1,http://loinc.org|2823-3,http://loinc.org|28245-9,http://loinc.org|2857-1,http://loinc.org|2885-2,http://loinc.org|29463-7,http://loinc.org|2947-0,http://loinc.org|2951-2,http://loinc.org|3094-0,http://loinc.org|32167-9,http://loinc.org|32207-3,http://loinc.org|32465-7,http://loinc.org|32623-1,http://loinc.org|33728-7,http://loinc.org|33756-8,http://loinc.org|33762-6,http://loinc.org|33914-3,http://loinc.org|33959-8,http://loinc.org|38208-5,http://loinc.org|38265-5,http://loinc.org|38483-4,http://loinc.org|39156-5,http://loinc.org|44667-4,http://loinc.org|44963-7,http://loinc.org|4544-3,http://loinc.org|4548-4,http://loinc.org|46240-8,http://loinc.org|46288-7,http://loinc.org|48065-7,http://loinc.org|49765-1,http://loinc.org|55277-8,http://loinc.org|5767-9,http://loinc.org|5770-3,http://loinc.org|5778-6,http://loinc.org|57905-2,http://loinc.org|5792-7,http://loinc.org|5794-3,http://loinc.org|5797-6,http://loinc.org|5799-2,http://loinc.org|5802-4,http://loinc.org|5803-2,http://loinc.org|5804-0,http://loinc.org|5811-5,http://loinc.org|5902-2,http://loinc.org|59032-3,http://loinc.org|5905-5,http://loinc.org|59408-5,http://loinc.org|59557-9,http://loinc.org|59576-9,http://loinc.org|6075-6,http://loinc.org|6082-2,http://loinc.org|6085-5,http://loinc.org|6095-4,http://loinc.org|6106-9,http://loinc.org|6158-0,http://loinc.org|6189-5,http://loinc.org|6206-7,http://loinc.org|6246-3,http://loinc.org|6248-9,http://loinc.org|6273-7,http://loinc.org|6276-0,http://loinc.org|6298-4,http://loinc.org|6299-2,http://loinc.org|6301-6,http://loinc.org|63513-6,http://loinc.org|65750-2,http://loinc.org|66519-0,http://loinc.org|66524-0,http://loinc.org|66529-9,http://loinc.org|66534-9,http://loinc.org|6690-2,http://loinc.org|6768-6,http://loinc.org|6833-8,http://loinc.org|6844-5,http://loinc.org|69453-9,http://loinc.org|704-7,http://loinc.org|706-2,http://loinc.org|711-2,http://loinc.org|713-8,http://loinc.org|718-7,http://loinc.org|71802-3,http://loinc.org|72106-8,http://loinc.org|72166-2,http://loinc.org|72514-3,http://loinc.org|7258-7,http://loinc.org|731-0,http://loinc.org|736-9,http://loinc.org|742-7,http://loinc.org|751-8,http://loinc.org|75325-1,http://loinc.org|76690-7,http://loinc.org|770-8,http://loinc.org|77606-2,http://loinc.org|777-3,http://loinc.org|785-6,http://loinc.org|786-4,http://loinc.org|787-2,http://loinc.org|788-0,http://loinc.org|789-8,http://loinc.org|80382-5,http://loinc.org|80383-3,http://loinc.org|8302-2,http://loinc.org|8310-5,http://loinc.org|8331-1,http://loinc.org|8478-0,http://loinc.org|85318-4,http://loinc.org|85319-2,http://loinc.org|85337-4,http://loinc.org|85339-0,http://loinc.org|85352-3,http://loinc.org|85354-9,http://loinc.org|88020-3,http://loinc.org|88021-1,http://loinc.org|88040-1,http://loinc.org|88262-1,http://loinc.org|8867-4,http://loinc.org|89579-7,http://loinc.org|91148-7,http://loinc.org|92130-4,http://loinc.org|92131-2,http://loinc.org|92134-6,http://loinc.org|92138-7,http://loinc.org|92139-5,http://loinc.org|92140-3,http://loinc.org|92141-1,http://loinc.org|92142-9,http://loinc.org|9279-1,http://loinc.org|94040-3,http://loinc.org|94531-1,http://loinc.org|9843-4,http://loinc.org|99999-0" 42929 | |
| - name: Download Observation Resources of male Patients | |
| run: .github/scripts/download-resources-query.sh Observation "patient.gender=male" 20466 | |
| - name: Download Observation Resources of male Patients Sorted by ID | |
| run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_id" 20466 | |
| - name: Download Observation Resources of male Patients Sorted Ascending by Last Updated | |
| run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "_lastUpdated" 20466 | |
| - name: Download Observation Resources of male Patients Sorted Descending by Last Updated | |
| run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=male" "-_lastUpdated" 20466 | |
| - name: Download Laboratory Observation Resources Sorted by ID | |
| run: .github/scripts/download-resources-query-sort.sh Observation "category=laboratory" "_id" 29206 | |
| - name: Download Laboratory Observation Resources Sorted Ascending by Last Updated | |
| run: .github/scripts/download-resources-query-sort.sh Observation "category=laboratory" "_lastUpdated" 29206 | |
| - name: Download Observation Resources of female Patients | |
| run: .github/scripts/download-resources-query.sh Observation "_count=500&patient.gender=female" 22463 | |
| - name: Download Observation Resources of the year 1970 | |
| run: .github/scripts/download-resources-query.sh Observation "date=1970" 59 | |
| - name: Download Observation Resources of the year 1970 Sorted by ID | |
| run: .github/scripts/download-resources-query-sort.sh Observation "date=1970" "_id" 59 | |
| - name: Download Observation Resources of the year 1980 | |
| run: .github/scripts/download-resources-query.sh Observation "date=1980" 0 | |
| - name: Download Observation Resources of the year 1980 Sorted by ID | |
| run: .github/scripts/download-resources-query-sort.sh Observation "date=1980" "_id" 0 | |
| - name: Download Observation Resources of the year 1990 | |
| run: .github/scripts/download-resources-query.sh Observation "date=1990" 19 | |
| - name: Download Observation Resources of the year 2000 | |
| run: .github/scripts/download-resources-query.sh Observation "date=2000" 101 | |
| - name: Download Observation Resources of the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=2010" 995 | |
| - name: Download Observation Resources of the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=2020" 17419 | |
| - name: Download Observation Resources of the year 2020 Sorted by ID | |
| run: .github/scripts/download-resources-query-sort.sh Observation "date=2020" "_id" 17419 | |
| - name: Download Observation Resources not of the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=ne2020" 25510 | |
| - name: Download Observation Resources not of the year 2020 Sorted by ID | |
| run: .github/scripts/download-resources-query-sort.sh Observation "date=ne2020" "_id" 25510 | |
| - name: Download Observation Resources greater than the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=gt2010" 38486 | |
| - name: Download Observation Resources greater than the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=gt2020" 983 | |
| - name: Download Observation Resources less than the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=lt2010" 3448 | |
| - name: Download Observation Resources less than the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=lt2020" 24527 | |
| - name: Download Observation Resources greater equal the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=ge2010" 39481 | |
| - name: Download Observation Resources greater equal the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=ge2020" 18402 | |
| - name: Download Observation Resources less equal the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=le2010" 4443 | |
| - name: Download Observation Resources less equal the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=le2020" 41946 | |
| - name: Download Observation Resources that start after the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=sa2010" 38486 | |
| - name: Download Observation Resources that start after the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=sa2020" 983 | |
| - name: Download Observation Resources that end before the year 2010 | |
| run: .github/scripts/download-resources-query.sh Observation "date=eb2010" 3448 | |
| - name: Download Observation Resources that end before the year 2020 | |
| run: .github/scripts/download-resources-query.sh Observation "date=eb2020" 24527 | |
| - name: Check Observation Date Search | |
| run: .github/scripts/check-date-search.sh "Observation" | |
| - name: Check Encounter Date Search | |
| run: .github/scripts/check-date-search.sh "Encounter" | |
| - name: Check DiagnosticReport Date Search | |
| run: .github/scripts/check-date-search.sh "DiagnosticReport" | |
| - name: Download Observation Resources of female Patients Sorted Ascending | |
| run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "_lastUpdated" 22463 | |
| - name: Download Observation Resources of female Patients Sorted Descending | |
| run: .github/scripts/download-resources-query-sort.sh Observation "patient.gender=female" "-_lastUpdated" 22463 | |
| - name: Download Observation Resources - Including Patients | |
| run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:patient' -o Observation-Patient.ndjson | |
| - name: Download Observation Resources - Including Encounters and Patients | |
| run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:encounter&_include=Observation:patient' -o Observation-Encounter-Patient.ndjson | |
| - name: Download Observation Resources - Including Encounters and Encounter Patients | |
| run: blazectl --no-progress --server http://localhost:8080/fhir download Observation -q '_include=Observation:encounter&_include:iterate=Encounter:patient' -o Observation-Encounter-Encounter-Patient.ndjson | |
| - name: Download Condition Resources | |
| run: .github/scripts/download-resources.sh Condition | |
| - name: Download Condition Resources - Including Subjects | |
| run: blazectl --no-progress --server http://localhost:8080/fhir download Condition -q '_include=Condition:subject' -o Condition-Subject.ndjson | |
| - name: Download Condition Resources - Including Encounters | |
| run: blazectl --no-progress --server http://localhost:8080/fhir download Condition -q '_include=Condition:encounter' -o Condition-Encounter.ndjson | |
| - name: Download DiagnosticReport Resources | |
| run: .github/scripts/download-resources.sh DiagnosticReport | |
| - name: Download MedicationRequest Resources of Medications with code 854235 | |
| run: .github/scripts/download-resources-query.sh MedicationRequest "medication.code=1736854" 112 | |
| - name: Download MedicationRequest Resources of Medications with code 854235 Sorted Ascending | |
| run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "_lastUpdated" 112 | |
| - name: Download MedicationRequest Resources of Medications with code 854235 Sorted Descending | |
| run: .github/scripts/download-resources-query-sort.sh MedicationRequest "medication.code=1736854" "-_lastUpdated" 112 | |
| - name: Download MedicationRequest Resources - Including Medications | |
| run: blazectl --no-progress --server http://localhost:8080/fhir download MedicationRequest -q '_include=MedicationRequest:medication' -o MedicationRequest.ndjson | |
| - name: Download male Patient Resources having inpatient Encounters in 2010 | |
| run: .github/scripts/download-resources-query.sh Patient "gender=male&_has:Encounter:patient:class=IMP&_has:Encounter:patient:date=2010" 8 | |
| - name: Download female Patient Resources having inpatient Encounters in 2010 | |
| run: .github/scripts/download-resources-query.sh Patient "gender=female&_has:Encounter:patient:class=IMP&_has:Encounter:patient:date=2010" 11 | |
| - name: Download Observations using _elements=subject | |
| run: .github/scripts/download-observations-elements.sh | |
| - name: Download Observations of all Encounters using ID's | |
| run: .github/scripts/download-observations-of-all-encounters.sh | |
| - name: Search Observation _lastUpdated | |
| run: .github/scripts/search-patient-last-updated.sh | |
| - name: Search Observation _profile | |
| run: .github/scripts/search-observation-profile.sh | |
| - name: Search Compartment | |
| run: .github/scripts/search-compartment.sh | |
| - name: Evaluate CQL Query 1 | |
| run: .github/scripts/evaluate-measure.sh q1 56 | |
| - name: Evaluate CQL Query 1 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q1 56 | |
| - name: Evaluate CQL Query 1 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q1 56 | |
| - name: Evaluate CQL Query 1 on Individual Patients | |
| run: .github/scripts/evaluate-patient-q1-measure.sh | |
| - name: Evaluate CQL Query 2 | |
| run: .github/scripts/evaluate-measure.sh q2 42 | |
| - name: Evaluate CQL Query 2 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q2 42 | |
| - name: Evaluate CQL Query 2 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q2 42 | |
| - name: Evaluate CQL Query 4 | |
| run: .github/scripts/evaluate-measure.sh q4 0 | |
| - name: Evaluate CQL Query 4 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q4 0 | |
| - name: Evaluate CQL Query 4 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q4 0 | |
| - name: Evaluate CQL Query 7 | |
| run: .github/scripts/evaluate-measure.sh q7 81 | |
| - name: Evaluate CQL Query 7 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q7 81 | |
| - name: Evaluate CQL Query 7 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q7 81 | |
| - name: Evaluate CQL Query 14 | |
| run: .github/scripts/evaluate-measure.sh q14 96 | |
| - name: Evaluate CQL Query 14 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q14 96 | |
| - name: Evaluate CQL Query 14 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q14 96 | |
| - name: Evaluate CQL Query 17 | |
| run: .github/scripts/evaluate-measure.sh q17 120 | |
| - name: Evaluate CQL Query 17 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q17 120 | |
| - name: Evaluate CQL Query 17 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q17 120 | |
| - name: Evaluate CQL Query 20 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q20-stratifier-city 120 | |
| - name: Evaluate CQL Query 21 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q21-stratifier-city-of-only-women 64 | |
| - name: Evaluate CQL Query 26 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q26-stratifier-bmi 120 | |
| - name: Evaluate CQL Query 27 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q27-stratifier-calculated-bmi 120 | |
| - name: Evaluate CQL Query 32 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl-stratifier.sh q32-stratifier-underweight 120 | |
| - name: Evaluate CQL Query 36 | |
| run: .github/scripts/evaluate-measure.sh q36-parameter 86 | |
| - name: Evaluate CQL Query 36 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q36-parameter 86 | |
| - name: Evaluate CQL Query 34 | |
| run: .github/scripts/evaluate-measure.sh q37-overlaps 24 | |
| - name: Evaluate CQL Query 34 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q37-overlaps 24 | |
| - name: Evaluate CQL Query 34 - Subject List | |
| run: .github/scripts/evaluate-measure-subject-list.sh q37-overlaps 24 | |
| - name: Evaluate CQL Query 46 | |
| run: .github/scripts/evaluate-measure.sh q46-between-date 19 | |
| - name: Evaluate CQL Query 46 using Blazectl | |
| run: .github/scripts/evaluate-measure-blazectl.sh q46-between-date 19 | |
| - name: Forwarded Header HTTPS | |
| run: .github/scripts/forwarded-header.sh https | |
| - name: Forwarded Header HTTP | |
| run: .github/scripts/forwarded-header.sh http | |
| - name: X-Forwarded Headers HTTPS | |
| run: .github/scripts/x-forwarded-headers.sh https | |
| - name: X-Forwarded Headers HTTP | |
| run: .github/scripts/x-forwarded-headers.sh http | |
| - name: Delete | |
| run: .github/scripts/delete.sh | |
| - name: Delete Violating Referential Integrity | |
| run: .github/scripts/check-referential-integrity-for-delete.sh 409 | |
| - name: Batch | |
| run: .github/scripts/batch.sh | |
| - name: Batch Metadata | |
| run: .github/scripts/batch-metadata.sh | |
| - name: Transaction | |
| run: .github/scripts/transaction.sh | |
| - name: Transaction Read/Write | |
| run: .github/scripts/transaction-rw.sh | |
| - name: Transactional Delete Preserving Referential Integrity | |
| run: .github/scripts/transactional-delete.sh | |
| - name: Transaction with Invalid (Null) Resource | |
| run: .github/scripts/transaction-null-resource.sh | |
| - name: OPTIONS | |
| run: curl -f -XOPTIONS http://localhost:8080/fhir/metadata | |
| - name: Health | |
| run: curl -f http://localhost:8080/health | |
| - name: Health - HEAD | |
| run: curl -f --head http://localhost:8080/health | |
| - name: Not Acceptable | |
| run: .github/scripts/not-acceptable.sh | |
| - name: Conditional Update If-None-Match | |
| run: .github/scripts/conditional-update-if-none-match.sh | |
| - name: GraphQL Patient | |
| run: .github/scripts/graphql.sh Patient | |
| - name: GraphQL Observation | |
| run: .github/scripts/graphql.sh Observation | |
| - name: Link Header Encoding | |
| run: .github/scripts/link-header-encoding.sh | |
| - name: Paging uses a Stable Snapshot of the Database (Patient) | |
| run: .github/scripts/follow-patient-next-link-after-write.sh | |
| - name: Paging uses a Stable Snapshot of the Database (system) | |
| run: .github/scripts/follow-system-next-link-after-write.sh | |
| - name: Create Patient | |
| run: .github/scripts/create-patient.sh | |
| - name: Read Ignores T | |
| run: .github/scripts/read-ignores-t.sh | |
| - name: Patient Everything | |
| run: .github/scripts/patient-everything.sh | |
| - name: Patient Everything with Date Range | |
| run: .github/scripts/patient-everything-date-range.sh | |
| - name: Patient Everything Paged | |
| run: .github/scripts/patient-everything-paged.sh | |
| - name: Patient Identical Update | |
| run: .github/scripts/patient-identical-update.sh | |
| - name: System History | |
| run: .github/scripts/system-history-paged.sh | |
| - name: Patient History | |
| run: .github/scripts/patient-history-paged.sh | |
| - name: Patient X79746011X History | |
| run: .github/scripts/single-patient-history.sh X79746011X | |
| - name: History Paging uses a Stable Snapshot of the Database (system) | |
| run: .github/scripts/follow-system-history-next-link-after-write.sh | |
| - name: History Paging uses a Stable Snapshot of the Database (Patient) | |
| run: .github/scripts/follow-patient-history-next-link-after-write.sh | |
| - name: History Paging uses a Stable Snapshot of the Database (single Patient) | |
| run: .github/scripts/follow-single-patient-history-next-link-after-write.sh | |
| - name: Prometheus Metrics | |
| run: .github/scripts/test-metrics.sh | |
| if: ${{ matrix.variant == 'standalone' }} | |
| - name: Prometheus Metrics - Blaze 1 | |
| run: curl -f http://localhost:8081/metrics | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Prometheus Metrics - Blaze 2 | |
| run: curl -f http://localhost:8082/metrics | |
| if: ${{ matrix.variant == 'distributed' }} | |
| - name: Docker Stats | |
| run: docker stats --no-stream | |
| integration-test-synthea-1000: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e DB_BLOCK_CACHE_SIZE=2048 -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Check Referential Integrity Enforced | |
| run: .github/scripts/check-referential-integrity-enforced.sh | |
| - name: Download Synthea Test Data | |
| run: wget https://speicherwolke.uni-leipzig.de/index.php/s/kDsa2ifeMFdqK35/download/synthea-1000.tar | |
| - name: Create Synthea Test Data Dir | |
| run: mkdir test-data-synthea-1000 | |
| - name: Unpack Synthea Test Data | |
| run: tar -C test-data-synthea-1000 -xf synthea-1000.tar | |
| - name: Load Data | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload test-data-synthea-1000 | |
| - name: Check Total-Number of Resources are 1099594 | |
| run: .github/scripts/check-total-number-of-resources.sh 1099594 | |
| - name: Count the number of Patients with Stress Conditions at Inpatient Encounters using FHIR Search | |
| run: .github/scripts/count-patients.sh Condition "code=http://snomed.info/sct|73595000&encounter.class=http://terminology.hl7.org/CodeSystem/v3-ActCode|IMP" 13 | |
| - name: Count the number of Patients with Stress Conditions at Inpatient Encounters using CQL | |
| run: .github/scripts/evaluate-measure-blazectl.sh inpatient-stress 13 | |
| - name: Condition Code Stratifier | |
| run: .github/scripts/evaluate-measure-blazectl-stratifier.sh stratifier-condition-code 51599 | |
| - name: Patient Everything Too Costly | |
| run: .github/scripts/patient-everything-too-costly.sh | |
| - name: Patient Everything Paged | |
| run: .github/scripts/patient-everything-paged-1000.sh | |
| - name: Docker Stats | |
| run: docker stats --no-stream | |
| not-enforcing-referential-integrity-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENFORCE_REFERENTIAL_INTEGRITY=false -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Check Referential Integrity Not Enforced | |
| run: .github/scripts/check-referential-integrity-not-enforced.sh | |
| - name: Load Data | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload -c1 .github/test-data/etl | |
| - name: Check Total-Number of Resources are 5 | |
| run: .github/scripts/check-total-number-of-resources.sh 5 | |
| - name: Check Referential Integrity Not Enforced For Delete | |
| run: .github/scripts/check-referential-integrity-for-delete.sh 204 | |
| admin-api-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENABLE_ADMIN_API=true -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Create Invalid Jobs | |
| run: .github/scripts/admin-api/create-invalid-jobs.sh | |
| # This test uploads many small transactions in order to show that Blaze can handle many small requests containing | |
| # chunked payload blazectl uses. Versions of Blaze from 0.13.2 to 0.15.3, starting with the migration to Jetty, had | |
| # the problem that the JSON parser did not read the entire inputstream so that terminal chunks could remain, which | |
| # caused Jetty to close the stream. | |
| small-transactions-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Generate Test Data | |
| run: mkdir .github/test-data/small-txs && .github/scripts/gen-bundle-ndjson.sh > .github/test-data/small-txs/bundles.ndjson | |
| - name: Load Data Sequentially | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload -c 1 .github/test-data/small-txs | |
| - name: Load Data with Concurrency 2 | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload -c 2 .github/test-data/small-txs | |
| big-transaction-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Load Data | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/big-tx | |
| evaluate-measure-timeout-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e FHIR_OPERATION_EVALUATE_MEASURE_TIMEOUT=10 -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Load Data | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea | |
| - name: Evaluate CQL Query 1 | |
| run: .github/scripts/evaluate-measure-timeout.sh q1 | |
| include-without-referential-integrity-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENFORCE_REFERENTIAL_INTEGRITY=false -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Test Include | |
| run: .github/scripts/include-without-referential-integrity.sh | |
| chaining-without-referential-integrity-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e ENFORCE_REFERENTIAL_INTEGRITY=false -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Test Chaining | |
| run: .github/scripts/chaining-without-referential-integrity.sh | |
| # Test that a transaction can create a transaction bundle with references that will be taken "as-is" and not tried to | |
| # resolve to existing resources | |
| bundle-with-references-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Load Data | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/bundle-with-references | |
| jepsen-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Java | |
| uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| cli: '1.11.2.1446' | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-temurin-17-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }} | |
| - name: APT Update | |
| run: sudo apt-get update | |
| - name: Install Gnuplot | |
| run: sudo apt-get install gnuplot | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Jepsen Register Test | |
| run: make -C modules/jepsen register-test-fast | |
| openid-auth-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Keycloak | |
| run: docker-compose -f .github/openid-auth-test/docker-compose.yml up -d keycloak | |
| - name: Wait for Keycloak | |
| run: .github/scripts/wait-for-url.sh http://localhost:8090/health/ready | |
| - name: Run Blaze | |
| run: docker-compose -f .github/openid-auth-test/docker-compose.yml up -d blaze | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs Keycloak | |
| run: docker-compose -f .github/openid-auth-test/docker-compose.yml logs keycloak | |
| - name: Docker Logs Blaze | |
| run: docker-compose -f .github/openid-auth-test/docker-compose.yml logs blaze | |
| - name: Unauthenticated Request | |
| run: test "MSG_AUTH_REQUIRED" = "$(curl -s http://localhost:8080/fhir | jq -r .issue[0].details.coding[0].code)" | |
| - name: Authenticated Request | |
| run: .github/scripts/authenticated-request.sh | |
| custom-search-parameters-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Keycloak and Blaze | |
| run: docker-compose -f .github/custom-search-parameters-test/docker-compose.yml up -d | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs Blaze | |
| run: docker-compose -f .github/custom-search-parameters-test/docker-compose.yml logs blaze | |
| - name: Create Patient | |
| run: .github/custom-search-parameters-test/create-patient.sh | |
| - name: Search Patient | |
| run: .github/custom-search-parameters-test/search-patient.sh | |
| doc-copy-data-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Test Setup | |
| run: docker-compose -f docs/data-sync/copy/docker-compose.yml -f .github/doc-copy-data-test/docker-compose.override.yml up -d | |
| - name: Wait for Source Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Load Data Into Source Blaze | |
| run: blazectl --no-progress --server http://localhost:8080/fhir upload .github/test-data/synthea | |
| - name: Wait for Destination Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8082/health | |
| - name: Copy All Resources from Source to Destination | |
| run: scripts/copy-data.sh http://localhost:8080/fhir http://localhost:8082/fhir | |
| - name: Download Source Patients | |
| run: blazectl download --server http://localhost:8080/fhir Patient | jq -c 'del(.meta.versionId) | del(.meta.lastUpdated)' > src-patients.ndjson | |
| - name: Download Destination Patients | |
| run: blazectl download --server http://localhost:8082/fhir Patient | jq -c 'del(.meta.versionId) | del(.meta.lastUpdated)' > dst-patients.ndjson | |
| - name: Compare Source and Destination Patients | |
| run: diff src-patients.ndjson dst-patients.ndjson | |
| big-binary-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -e DB_RESOURCE_CACHE_SIZE=0 -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Generate Large Binary Resources (JSON and XML) | |
| run: .github/scripts/generate-large-binary-resource.sh | |
| - name: Post Large Binary JSON Resource | |
| run: curl -f -H Content-Type:application/fhir+json -H Prefer:return=minimal -d @large-binary.json http://localhost:8080/fhir/Binary | |
| - name: Post Large Binary XML Resource | |
| run: curl -f -H Content-Type:application/fhir+xml -H Prefer:return=minimal -d @large-binary.xml http://localhost:8080/fhir/Binary | |
| - name: Download Both Resources | |
| run: test "2" = "$(curl -s http://localhost:8080/fhir/Binary | jq .total)" | |
| frontend-test: | |
| needs: [ build, build-frontend ] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Setup Node | |
| uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: 21 | |
| - name: Install Blazectl | |
| run: .github/scripts/install-blazectl.sh | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Download Blaze Frontend Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-frontend-image | |
| path: /tmp | |
| - name: Load Blaze Frontend Image | |
| run: docker load --input /tmp/blaze-frontend.tar | |
| # https://bugs.webkit.org/show_bug.cgi?id=160504 | |
| - name: Add Blaze Localhost Entry needed for Webkit | |
| run: | | |
| sudo echo "127.0.0.1 blaze.localhost" | sudo tee -a /etc/hosts | |
| sudo echo "127.0.0.1 keycloak.localhost" | sudo tee -a /etc/hosts | |
| - name: Generate Ingress Certificates | |
| run: make build-ingress | |
| - name: Run Keycloak | |
| run: docker-compose -f modules/frontend-e2e/docker-compose.yml up -d keycloak | |
| - name: Sleep 20 Seconds | |
| run: sleep 20 | |
| - name: Run Everything Else | |
| run: docker-compose -f modules/frontend-e2e/docker-compose.yml up -d | |
| - name: Sleep 30 Seconds | |
| run: sleep 30 | |
| - name: Docker Logs | |
| run: docker-compose -f modules/frontend-e2e/docker-compose.yml logs | |
| - name: Load Data | |
| run: modules/frontend-e2e/upload.sh | |
| - name: Check Frontend | |
| run: .github/scripts/check-frontend.sh | |
| - name: Check Column Family resource-as-of-index | |
| run: .github/scripts/admin-api/column-family-metadata.sh resource-as-of-index | |
| - name: Check Column Family search-param-value-index | |
| run: .github/scripts/admin-api/column-family-metadata.sh search-param-value-index | |
| - name: Download Patient Resources | |
| run: modules/frontend-e2e/download-patient-resources.sh | |
| - name: Install Playwright | |
| run: make -C modules/frontend-e2e install | |
| - name: Run Playwright Tests | |
| run: make -C modules/frontend-e2e test | |
| - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4 | |
| with: | |
| name: playwright-report | |
| path: modules/frontend-e2e/playwright-report/ | |
| missing-resource-content-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Create a Data Dir | |
| run: mkdir data | |
| - name: Run Blaze | |
| run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v "$(pwd)/data:/app/data" blaze:latest | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Docker Logs | |
| run: docker logs blaze | |
| - name: Create Patient | |
| run: .github/scripts/create-patient-0.sh | |
| - name: Stop Blaze | |
| run: docker stop blaze | |
| - name: Remove Resource Database | |
| run: rm -r data/resource | |
| - name: Start Blaze Again | |
| run: docker start blaze | |
| - name: Wait for Blaze | |
| run: .github/scripts/wait-for-url.sh http://localhost:8080/health | |
| - name: Fetch Patient Expecting an Error | |
| run: .github/scripts/fetch-resource-0-with-missing-resource-content.sh | |
| jepsen-distributed-test: | |
| needs: build | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Setup Java | |
| uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: 'temurin' | |
| java-version: '21' | |
| - name: Setup Clojure | |
| uses: DeLaGuardo/setup-clojure@master | |
| with: | |
| cli: '1.11.2.1446' | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Cache Local Maven Repo | |
| uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| with: | |
| path: ~/.m2/repository | |
| key: ${{ runner.os }}-temurin-17-maven-jepsen-${{ hashFiles('modules/jepsen/deps.edn') }} | |
| - name: APT Update | |
| run: sudo apt-get update | |
| - name: Install Gnuplot | |
| run: sudo apt-get install gnuplot | |
| - name: Download Blaze Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-image | |
| path: /tmp | |
| - name: Load Blaze Image | |
| run: docker load --input /tmp/blaze.tar | |
| - name: Run Kafka, Cassandra and Blaze | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml up -d | |
| - name: Wait for Blaze 1 | |
| run: .github/scripts/wait-for-url.sh http://localhost:8081/metrics | |
| - name: Wait for Blaze 2 | |
| run: .github/scripts/wait-for-url.sh http://localhost:8082/metrics | |
| - name: Docker Logs Kafka | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs kafka | |
| - name: Docker Logs Cassandra 1 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs cassandra-1 | |
| - name: Docker Logs Cassandra 2 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs cassandra-2 | |
| - name: Docker Logs Blaze 1 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs blaze-1 | |
| - name: Docker Logs Blaze 2 | |
| run: docker-compose -f .github/distributed-test/docker-compose.yml logs blaze-2 | |
| - name: Docker Stats | |
| run: docker stats --no-stream | |
| - name: Check Capability Statement | |
| run: .github/scripts/check-capability-statement.sh | |
| - name: Jepsen Register Test | |
| run: make -C modules/jepsen register-test-slow | |
| - name: Docker Stats | |
| run: docker stats --no-stream | |
| push-image: | |
| if: github.event_name != 'pull_request' || (github.event.pull_request.base.repo.full_name == github.event.pull_request.head.repo.full_name) | |
| needs: | |
| - image-scan | |
| - integration-test | |
| - integration-test-synthea-1000 | |
| - not-enforcing-referential-integrity-test | |
| - admin-api-test | |
| - small-transactions-test | |
| - big-transaction-test | |
| - evaluate-measure-timeout-test | |
| - include-without-referential-integrity-test | |
| - chaining-without-referential-integrity-test | |
| - bundle-with-references-test | |
| - jepsen-test | |
| - jepsen-distributed-test | |
| - openid-auth-test | |
| - doc-copy-data-test | |
| - big-binary-test | |
| - frontend-test | |
| - missing-resource-content-test | |
| - custom-search-parameters-test | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| packages: write | |
| contents: write | |
| strategy: | |
| matrix: | |
| image: | |
| - name: ${{ github.event.repository.name }} | |
| context: . | |
| - name: ${{ github.event.repository.name }}-frontend | |
| context: modules/frontend | |
| env: | |
| dockerhub_username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Download Blaze Uberjar | |
| if: ${{ matrix.image.context == '.' }} | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: blaze-uberjar | |
| path: target | |
| - name: Setup Node | |
| if: ${{ matrix.image.context == 'modules/frontend' }} | |
| uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: 21 | |
| - name: Build Frontend | |
| if: ${{ matrix.image.context == 'modules/frontend' }} | |
| run: make build-frontend | |
| - name: Download Image | |
| uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4 | |
| with: | |
| name: ${{ matrix.image.name }}-image | |
| path: /tmp | |
| - name: Load Image | |
| run: docker load --input /tmp/${{ matrix.image.name }}.tar | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@68827325e0b33c7199eb31dd4e31fbe9023e06e3 # v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@d70bba72b1f3fd22344832f00baa16ece964efeb # v3 | |
| - name: Login to GHCR | |
| uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20 # v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: GHCR meta | |
| id: ghcr-meta | |
| uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81 # v5 | |
| with: | |
| images: | | |
| ghcr.io/${{ github.repository_owner }}/${{ matrix.image.name }} | |
| tags: | | |
| type=schedule | |
| type=ref,event=branch | |
| type=ref,event=pr | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| - name: Build and push to GHCR | |
| uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5 | |
| with: | |
| context: ${{ matrix.image.context }} | |
| platforms: linux/amd64,linux/arm64 | |
| push: true | |
| tags: ${{ steps.ghcr-meta.outputs.tags }} | |
| labels: ${{ steps.ghcr-meta.outputs.labels }} | |
| - name: Login to DockerHub | |
| if: ${{ env.dockerhub_username != '' }} | |
| uses: docker/login-action@e92390c5fb421da1463c202d546fed0ec5c39f20 # v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: DockerHub meta | |
| if: ${{ env.dockerhub_username != '' }} | |
| id: dockerhub-meta | |
| uses: docker/metadata-action@8e5442c4ef9f78752691e2d8f8d19755c6f78e81 # v5 | |
| with: | |
| images: | | |
| ${{ github.repository_owner }}/${{ matrix.image.name }} | |
| tags: | | |
| type=schedule | |
| type=ref,event=branch | |
| type=ref,event=pr | |
| type=semver,pattern={{version}} | |
| type=semver,pattern={{major}}.{{minor}} | |
| - name: Build and push to DockerHub | |
| if: ${{ env.dockerhub_username != '' }} | |
| uses: docker/build-push-action@2cdde995de11925a030ce8070c3d77a52ffcf1c0 # v5 | |
| with: | |
| context: ${{ matrix.image.context }} | |
| platforms: linux/amd64,linux/arm64 | |
| push: true | |
| tags: ${{ steps.dockerhub-meta.outputs.tags }} | |
| labels: ${{ steps.dockerhub-meta.outputs.labels }} | |
| release: | |
| if: github.ref_type == 'tag' | |
| needs: | |
| - push-image | |
| runs-on: ubuntu-22.04 | |
| permissions: | |
| packages: write | |
| contents: write | |
| steps: | |
| - name: Release | |
| uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2 | |
| with: | |
| files: target/blaze-*-standalone.jar | |
| build-pages: | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Check out Git repository | |
| uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4 | |
| - name: Setup Node | |
| uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: 18 | |
| cache: npm | |
| cache-dependency-path: 'docs/package-lock.json' | |
| - name: Install dependencies | |
| working-directory: ./docs | |
| run: npm install | |
| - name: Build | |
| working-directory: ./docs | |
| env: | |
| DOCS_BASE: "/${{ github.event.repository.name }}/" | |
| run: npm run docs:build | |
| - name: Setup Pages | |
| uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5 | |
| - name: Upload artifact | |
| uses: actions/upload-pages-artifact@56afc609e74202658d3ffba0e8f6dda462b719fa # v3 | |
| with: | |
| path: docs/.vitepress/dist | |
| deploy-pages: | |
| if: github.ref == 'refs/heads/master' | |
| runs-on: ubuntu-22.04 | |
| needs: [ build-pages ] | |
| permissions: | |
| pages: write | |
| id-token: write | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| id: deployment | |
| uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4 |